[Home ] [Archive]   [ فارسی ]  
:: About :: Main :: Current Issue :: Archive :: Search :: Submit :: Contact ::
Main Menu
Home::
Journal Information::
Articles archive::
For Authors::
For Reviewers::
Registration::
Contact us::
Site Facilities::
::
Search in website

Advanced Search
..
Receive site information
Enter your Email in the following box to receive the site news and information.
..



 
..
:: Volume 11, Issue 1 (2024) ::
pgr 2024, 11(1): 15-36 Back to browse issues page
Comparison of Genetic Diversity Between Two Oat Species (Avena sativa and Avena fatua) Using Phenotypic Traits, Molecular Markers, and Chromosomal Parameters
Parastoo Zarei , Hedieh Badakhshan * , Ghader Mirzaghaderi
Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, Kurdistan, Iran , h.badakhshan@uok.ac.ir
Abstract:   (379 Views)
Evaluating genetic diversity in plant species is essential for crop improvement. This research compared the genetic diversity between common oat (Avena sativa) and wild oat (Avena fatua) using molecular markers, phenotypic traits, and chromosomal characteristics. SCoT and IRAP markers generated 283 and 117 bands, respectively. Both marker systems revealed higher polymorphism in wild oat compared to common oat. SCoT markers showed 65.37 percent polymorphism in wild oat versus 60.07 percent in common oat, while IRAP markers exhibited 76.07 and 69.23 percent polymorphism, respectively. Genetic diversity indices (Ne, He, and PIC) indicated slightly higher genetic diversity in wild oat for both marker systems, although the genetic distance between the two species was relatively low. Population structure analysis using Bayesian methods, Principal Coordinate Analysis (PCoA), and Analysis of Molecular Variance (AMOVA) consistently identified distinct subpopulations and significant genetic variation within species. Phenotypic trait analysis revealed significant differences among genotypes. Common oat genotypes generally exhibited greater plant height, while wild oat genotypes had higher 100-seed weight. Heatmap cluster analysis grouped genotypes into three clusters based on phenotypic traits. All genotypes were hexaploid but showed differences in chromosomal parameters such as total chromosome length, centromeric index, and dispersion index. However, no significant differences were found between common and wild oat species in these parameters. Principal Component Analysis (PCA) of chromosomal parameters explained 94.72 percent of the cumulative variance, with PC1 emphasizing centromere position and PC2 highlighting chromosomal asymmetry. This comprehensive study provides valuable insights for breeding and conservation strategies in oat species.
Keywords: Population Structure, Principal component analysis, Molecular variance analysis, Heatmap, IRAP, SCoT
Full-Text [PDF 913 kb]   (35 Downloads)    
Type of Study: Research | Subject: Molecular genetics
References
1. Achleitner, A., Tinker, N.A. Zechner, E. and Buerstmayr, H. (2008). Genetic diversity among oat varieties of worldwide origin and associations of AFLP markers with quantitative traits. Theoretical and Applied Genetics, 117: 1041-1053. [DOI:10.1007/s00122-008-0843-y]
2. Alikhani, L., Rahmani, M.S., Shabanian, N., Badakhshan, H. and Khadivi-Khub, A. (2014). Genetic variability and structure of Quercus brantii assessed by ISSR, IRAP and SCoT markers. Gene, 552(1): 176-183. [DOI:10.1016/j.gene.2014.09.034]
3. Amosova, A.V., Nosov, N.N., Gnutikov, A.A., Rodionov, A.V., Loskutov, I.G., Yurkevich, O.Y., Samatadze, T.E., Zoshchuk, S.A. and Muravenko, O.V. (2024). Genome variability in artificial allopolyploid hybrids of Avena sativa L. and Avena macrostachya Balansa ex Coss. et Durieu based on marker sequences of satellite DNA and the ITS1-5.8S rDNA Region. International Journal of Molecular Science, 25: 5534. [DOI:10.3390/ijms25105534]
4. Androsiuk, P., Eryka, S., Justyna, M., Wioleta, D. and Sopyła, K. (2023). The comparison of polymorphism among Avena species revealed by retrotransposon‑ based DNA markers and soluble carbohydrates in seeds. Journal of Applied Genetics, 64: 247-264. [DOI:10.1007/s13353-023-00748-w]
5. Arora, A., Kundu, S., Dilbaghi, N., Sharma, I. and Tiwari, R. (2014). Population structure and genetic diversity among Indian wheat varieties using microsatellite (SSR) markers. Australian Journal of Crop Science, 81: 281-1289.
6. Arora, A., Sood, V.K., Chaudhary, H.K., Banyal, D.K., Kumar, S., Devi, R., Kumari, A., Khushbu, P. and Yograj, S. (2021). Genetic diversity analysis of oat (Avena sativa) germplasm revealed by agro-morphological and SSR markers. Range Management and Agroforestry, 42: 38-48.
7. Azizi, E., Salehan, N., Rahbarian, R. and Masoomi, A. (2024). Cytogenetic analysis of different landraces of purslane (Portulaca oleracea L.). Plant Genetic Researches, 10(2): 35-46 (In Persian). http://dx.doi.org/10.22034/PGR.10.2.3 Aziznia, R., Badakhshan, H., Javadi, T. and Zamani, S. (2020). Assessment of diversity in barley genotypes (Hordeum vulgare L) based on beta-glucan content and ISSR markers. Plant Genetic Researches, 6(2): 97-110 (In Persian). [DOI:10.29252/pgr.6.2.97]
8. Badaeva, E.D., Shelukhina, O.Y., Dedkova, O.S., Loskutov, I.G. and Pukhalskiy, V.A. (2011). Comparative cytogenetic analysis of hexaploid Avena L species. Plant Genetics, 47: 783-795. [DOI:10.1134/S1022795411060068]
9. Boczkowska, M. and Tarczyk, E. (2013). Genetic diversity among Polish landraces of common oat (Avena sativa L). Genetic Resources and Crop Evolution, 60: 2157-2169. [DOI:10.1007/s10722-013-9984-1]
10. Boczkowska, M., Nowosielski, J., Nowosielska, D. and Podyma, W. (2014). Assessing genetic diversity in 23 early Polish oat cultivars based on molecular and morphological studies. Genetic Resources and Crop Evolution, 61: 927-941. [DOI:10.1007/s10722-014-0087-4]
11. Botstein, D., White, R.L., Skolnick, M. and Davis, R.W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32: 314-331.
12. Chňapek, M., Mikolášova, L., Vivodík, M., Gálová, Z., Hromadová, Z., Ražná, K. and Balážová, Ž. (2022). Genetic diversity of oat genotypes using SCoT markers. Biology and Life Science Forum, 11: 29. [DOI:10.3390/IECPS2021-11926]
13. Cieplak, M., Okon, S. and Werwinska, K. (2021). Genetic similarity of Avena sativa L varieties as an example of a narrow genetic pool of contemporary cereal species. Plants, 10: 1-10. [DOI:10.3390/plants10071424]
14. Collard, B.C.Y. and Mackill, D.J. (2009). Start Codon Targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Molecular Biology Reporter, 27: 86-93. [DOI:10.1007/s11105-008-0060-5]
15. Da-Silva, P.R., Milach, S.C.K. and Tisian, L.M. (2011). Transferability and utility of white oat (Avena sativa) microsatellite markers for genetic studies in black oat (Avena strigosa). Genetics and Molecular Research, 10: 2916-2923. [DOI:10.4238/2011.November.29.2]
16. Earl, D.A. and VonHoldt, B.M. (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4: 359-361. [DOI:10.1007/s12686-011-9548-7]
17. Ebadi-Almas, D., Karimzadeh, G. and Mirzaghaderi, G. (2012). Karyotypic variation and karyomorphology in Iranian endemic ecotypes of Plantago ovata forsk. Cytologia, 77: 215-223. [DOI:10.1508/cytologia.77.215]
18. Eltaher, S., Sallam, A., Belamkar, V., Emara, H.A., Nower, A.A., Salem, K.F.M., Poland, J. and Baenziger, P.S. (2018). Genetic diversity and population structure of F3:6 Nebraska winter wheat genotypes using genotyping-by-sequencing. Frontiers in Genetics, 91: 9. [DOI:10.3389/fgene.2018.00076]
19. Evanno, G., Regnaut, S. and Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology, 14: 2611-2620. [DOI:10.1111/j.1365-294X.2005.02553.x]
20. Fu, Y.B. (2018). Oat evolution revealed in the maternal lineages of 25 Avena species. Scientific Reports, 8(1): 4252. [DOI:10.1038/s41598-018-22478-4]
21. He, X. and Bjørnstad, Å. (2012). Diversity of North European oat analyzed by SSR, AFLP and DArT markers. Theoretical and Applied Genetics, 125: 57-70. [DOI:10.1007/s00122-012-1816-8]
22. Hosseini, S., Rahgozar, M.R. and Badakhshan, H. (2022). Study of genetic diversity of some Allium L. species based on ISSR markers in Kurdistan province. Plant Genetic Researches, 8(2): 57-68 (In Persian). [DOI:10.52547/pgr.8.2.5]
23. Ihsan, M., Nazir, N., Ghafoor, A., Khalil, A.A.K., Zahoor, M., Nisar, M., Khames, A., Ullah, R. and Shah, A.B. (2021). Genetic diversity in local and exotic Avena sativa (oat) germplasm using multivariate analysis. Agronomy, 1: 11-18. [DOI:10.3390/agronomy11091713]
24. Ihsan, M., Nisar, M., Nazir, N., Zahoor, M., Khalil, A.A.K., Ghafoor, A., Khan, A., Mothana, R.A., Ullah, R. and Ahmad, N. (2022). Genetic diversity in nutritional composition of oat (Avena sativa L) germplasm reported from Pakistan. Saudi Journal of Biological Sciences, 29: 1487-1500. [DOI:10.1016/j.sjbs.2021.11.023]
25. Jan, S.F., Khan, M.R., Iqbal, A., Khan, F.U. and Ali, S. (2020). Genetic diversity in exotic oat germplasm & resistance against barley yellow dwarf virus. Saudi Journal of Biological Sciences, 27: 2622-2631. [DOI:10.1016/j.sjbs.2020.05.042]
26. Jellen, E.N., Phillips, R.L. and Rines, H.W. (1993). C-banded karyotypes and polymorphisms in hexaploid oat accessions (Avena spp) using Wright's stain. Genome, 36: 1129-1137. [DOI:10.1139/g93-151]
27. Kalendar, R., Grob, T., Regina, M., Suoniemi, A. and Schulman, A. (1999). IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theoretical and Applied Genetics, 98: 704-711. [DOI:10.1007/s001220051124]
28. Kalendar, R., Flavell, A.J., Ellis, T.H.N., Sjakste, T., Moisy, C. and Schulman, A.H. (2011). Analysis of plant diversity with retrotransposon-based molecular markers. Heredity, 106: 520-530. [DOI:10.1038/hdy.2010.93]
29. Koroluk, A., Paczos-Grzeda, E., Sowa, S., Boczkowska, M. and Toporowska, J. (2022). Diversity of Polish oat cultivars with a glance at breeding history and perspectives. Agriculture, 12(10): 2423. [DOI:10.3390/agronomy12102423]
30. Ladizinsky, G. (1968). Chromosome rearrangements in the hexaploid oats. Notes and Comments, 69: 457-462.
31. Levan, A., Fredga, K. and Sandberg, A.A. (1964). Nomenclature for centromic position on chromosoms. Hereditas, 52: 201-220. [DOI:10.1111/j.1601-5223.1964.tb01953.x]
32. Li, R., Wang, S., Duan, L., Li, Z., Christoffers, M.J. and Mengistu, L.W. (2007). Genetic diversity of wild oat (Avena fatua) populations from China and the United States. Weed Science, 55: 95-101. [DOI:10.1614/WS-06-108.1]
33. Luo, C., He, X.H., Chen, H., Ou, S.J. and Gao, M.P. (2010). Analysis of diversity and relationships among mango cultivars using Start Codon Targeted (SCoT) markers. Biochemical Systematics and Ecology, 38: 1176-1184. [DOI:10.1016/j.bse.2010.11.004]
34. Mantel, N. (1967). The Detection of disease clustering and a generalized regression approach. Cancer Research, 27: 209-220.
35. Meyer, R.S. and Purugganan, M.D. (2013). Evolution of crop species: genetics of domestication and diversification. Nature Reviews Genetics, 14: 840-852. [DOI:10.1038/nrg3605]
36. Mirza, B., Shoaib, M., Ahmad, M. and Fu, Y.B. (2007). Genetic diversity in Pakistani populations of Avena fatua revealed by seed storage protein polymorphism. Communications in Biometry and Crop Science, 2: 41-48.
37. Mirzaghaderi, G. and Marzangi, K. (2015). IdeoKar: an ideogram constructing and karyotype analyzing software. Caryologia, 68: 31-35. [DOI:10.1080/00087114.2014.998526]
38. Montilla-Bascón, G., Sánchez-Martín, J., Rispail, N., Rubiales, D., Mur, L., Langdon, T., Griffiths, I., Howarth, C. and Prats, E. (2013). Genetic diversity and population structure among oat cultivars and landraces. Plant Molecular Biology Reporter, 31: 1305-1314. [DOI:10.1007/s11105-013-0598-8]
39. Nan, J., Ling, Y., An, J., Wang, T., Chai, M., Fu, J., Wang, G., Yang, C., Yang, Y. and Han, B. (2023). Genome resequencing reveals independent domestication and breeding improvement of naked oat. GigaScience, 12: 1-13. [DOI:10.1093/gigascience/giad061]
40. Nasrollahi, S., Badakhshan, H. and Sadeghi, A. (2019). Analyzing sunn pest resistance in bread wheat genotypes using phenotypic characteristics and molecular markers. Physiology and Molecular Biology of Plants, 25: 765-778. [DOI:10.1007/s12298-019-00662-8]
41. Nikoloudakis, N., Bladenopoulos, K. and Katsiotis, A. (2016). Structural patterns and genetic diversity among oat (Avena) landraces assessed by microsatellite markers and morphological analysis. Genetic Resources and Crop Evolution, 63: 801-811. [DOI:10.1007/s10722-015-0284-9]
42. Paczos-Grzeda, E. and Bednarek, P.T. (2014). Comparative analysis of hexaploid Avena species using REMAP and ISSR methods. Turkish Journal of Botany, 38: 1103-1111. [DOI:10.3906/bot-1403-10]
43. Paknia, R. and Karimzadeh, G. (2011). Karyotypic study and chromosome evolution in some Iranian local onion populations. Journal of Plant Physiology and Breeding, 1(1): 49-62.
44. Peakall, R. and Smouse, P.E. (2012). GenAlEx 6.5: genetic analysis in Excel population genetic software for teaching and research-an update. Bioinformatics, 28: 2537-2539. [DOI:10.1093/bioinformatics/bts460]
45. Peng, Y., Zhou, P., Zhao, J., Li, J., Lai, S., Tinker, A., Liao, S. and Id, H.Y. (2018). Phylogenetic relationships in the genus Avena based on the nuclear Pgk1 gene. PLoS One, 13: 1-18. [DOI:10.1101/351866]
46. Porebski, S., Bailey, L.G. and Baum, B.R. (1997). Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Molecular Biology Reporter, 15: 8-15. [DOI:10.1007/BF02772108]
47. Powell, W., Morgante, M., Andre, C., Hanafey, M., Vogel, J., Tingey, S. and Rafalski, A. (1996). The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplas analysis. Molecular Breeding, 2: 225-238. [DOI:10.1007/BF00564200]
48. Pritchard, J.K., Stephens, M. and Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155: 945-959. [DOI:10.1093/genetics/155.2.945]
49. Rahmani, M.S., Shabanian, N., Khadivi-Khub, A., Woeste, K.E., Badakhshan, H. and Alikhani, L. (2015). Population structure and genotypic variation of Crataegus pontica inferred by molecular markers. Gene, 572(1): 123-129. [DOI:10.1016/j.gene.2015.07.001]
50. Romero Zarco, C. (1986). A new method for estimating karyotype asymmetry. Taxon, 35: 526-530. [DOI:10.2307/1221906]
51. Sanchez-Martin, J., Mur, L.A.J., Rubiales, D. and Prats, E. (2012). Targeting sources of drought tolerance within an Avena spp collection through multivariate approaches. Planta, 236: 1529-1545. [DOI:10.1007/s00425-012-1709-8]
52. Tanhuanpää, P., Kalendar, R., Laurila, J., Schulman, A. H., Manninen, O. and Kiviharju, E. (2006). Generation of SNP markers for short straw in oat (Avena sativa L). Genome, 49: 282-287. [DOI:10.1139/g05-100]
53. Stebbins, G.L. (1971) Chromosomal Evolution in Higher Plants. Edward Arnold LTD, London, UK.
54. Tomás, D., Rodrigues, J., Varela, A., Veloso, M.M., Viegas, W. and Silva, M. (2016). Use of repetitive sequences for molecular and cytogenetic characterization of Avena species from Portugal. International Journal of Molecular Sciences, 17: 1-14. [DOI:10.3390/ijms17020203]
55. Tomaszewska, P., Schwarzacher, T. and Heslop-harrison, J.S.P. (2022). Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids. Frontiers in Plant Science, 1: 21. [DOI:10.1101/2022.08.23.504991]
56. van de Wouw, M., van Hintum, T., Kik, C., van Treuren, R. and Visser, B. (2010). Genetic diversity trends in twentieth century crop cultivars: A meta analysis. Theoretical and Applied Genetics, 120: 1241-1252. [DOI:10.1007/s00122-009-1252-6]
57. Yan, H., Zhou, P., Peng, Yun, Bekele, W.A., Ren, C., Tinker, N.A. and Peng, Y. (2020). Genetic diversity and genome-wide association analysis in Chinese hulless oat germplasm. Theoretical and Applied Genetics, 133: 3365-3380. [DOI:10.1007/s00122-020-03674-1]
Send email to the article author



XML   Persian Abstract   Print


Download citation:
BibTeX | RIS | EndNote | Medlars | ProCite | Reference Manager | RefWorks
Send citation to:

Zarei P, Badakhshan H, Mirzaghaderi G. Comparison of Genetic Diversity Between Two Oat Species (Avena sativa and Avena fatua) Using Phenotypic Traits, Molecular Markers, and Chromosomal Parameters. pgr 2024; 11 (1) :15-36
URL: http://pgr.lu.ac.ir/article-1-314-en.html


Rights and permissions
Creative Commons License This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Volume 11, Issue 1 (2024) Back to browse issues page
پژوهش های ژنتیک گیاهی Plant Genetic Researches
Persian site map - English site map - Created in 0.07 seconds with 38 queries by YEKTAWEB 4657